Can the 3D viewport display animated, textured material alpha)?
I use OpenGL constantly unless Forced to do otherwise.  I've also used it to fade out alpha layered texture pretty much as per your question, albeit with a 'mirror' or two.  You may have already done this, but others may find this useful.



The method is always to animate everything in the 3D window but place the textured model to be faded out in it's own layer.  This allows precise placement/scaling etc.  Objects that will conceal the fading object when it moves behind can be either duplicated in the extra layer, or masks setup to conceal it.

The cloud in this case is our fading object.

Once set up and animating properly, switch off the extra (cloud) layer and render the rest.

We render the cloud's layer next, only output that to alpha layered PNG files, and INTO A SEPERATE FOLDER!  Ensure you are indeed rendering with an alpha layer. (transparency)  At near top left of the 3D window is the "Render" drop-down.  "Render OpenGL image" most often gives you what's going to end up on the video.

Reset your output to it's final rendering folder, file type etc, and ensure the "Post output " is set to "Sequencer".

Go to the Video Editor and bring in the main video render onto the lower strip, the Alpha layered PNG files (as an image) onto one above it, and set the upper strip to "Alpha Over"

All that remains is to set keyframes on the upper strip to fade it in and out at the appropriate frame numbers.

Render that.  All of the renders only takes seconds, including the final one which of course must be from Blender's internal Renderer.

Hope this solves your problem...

PS:  It's also possible to mix the PNG video strip with a "Scene" strip and get the same result.  Unfortunately that has given me some grief in the past so I prefer to use two video strips.